ltrparser

Functions to identify and parse LTR sequences from HIV integration site and gene therapy samples.

Setup

Check the config/hiv.config.tsv file to make sure Bowtie indexes are in the correct location. You will need to set "Host" index for all samples, but only set "Viral" index if you want to map against an HIV database (e.g. for HIV Integration site data).

Running Tests

From the project directory, run:

cd R/

Rscript test.R

This will run the script on samples described in the file testdata/testdata.tsv using the parameters in the config/hiv.config.tsv config file.

CSV and PDF files created will be placed in testdata/demo/csv and testdata/demo/pdf, respectively (they will also already be there upon download but the script will recreate them).

Running on Real Data

To run the script on real data, modify or copy the testdata/testdata.tsv file and/or the R/test.R script to run the script on different input files and/or using different input parameters.